Maps creator
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@85657 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
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@ -1,48 +1,27 @@
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package org.gcube.dataanalysis.geo.algorithms;
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import it.cnr.aquamaps.CSquare;
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import it.geosolutions.geonetwork.util.GNInsertConfiguration;
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import it.geosolutions.geoserver.rest.encoder.GSLayerEncoder;
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import it.geosolutions.geoserver.rest.encoder.feature.GSFeatureTypeEncoder;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.List;
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import java.util.UUID;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
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import org.gcube.spatial.data.geonetwork.LoginLevel;
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import org.gcube.spatial.data.geonetwork.configuration.Configuration;
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import org.gcube.spatial.data.geonetwork.iso.GcubeISOMetadata;
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import org.gcube.spatial.data.geonetwork.iso.Thesaurus;
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import org.gcube.spatial.data.gis.GISInterface;
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import org.gcube.dataanalysis.geo.meta.PolyMapMetadata;
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import org.gcube.spatial.data.gis.model.report.PublishResponse;
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import org.geotoolkit.metadata.iso.extent.DefaultExtent;
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import org.hibernate.SessionFactory;
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import org.opengis.metadata.citation.PresentationForm;
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import org.opengis.metadata.identification.TopicCategory;
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import org.opengis.metadata.spatial.GeometricObjectType;
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import org.opengis.metadata.spatial.TopologyLevel;
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import scala.collection.Iterator;
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public class MapsCreator extends StandardLocalExternalAlgorithm {
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public abstract class MapsCreator extends StandardLocalExternalAlgorithm {
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private static final String crs = "GEOGCS[\"WGS 84\", DATUM[\"World Geodetic System 1984\", SPHEROID[\"WGS 84\", 6378137.0, 298.257223563, AUTHORITY[\"EPSG\",\"7030\"]]," + "AUTHORITY[\"EPSG\",\"6326\"]], PRIMEM[\"Greenwich\", 0.0, AUTHORITY[\"EPSG\",\"8901\"]], UNIT[\"degree\", 0.017453292519943295]," + "AXIS[\"Geodetic longitude\", EAST], AXIS[\"Geodetic latitude\", NORTH], AUTHORITY[\"EPSG\",\"4326\"]]";
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static String databaseParameterName = "FishBase";
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static String databaseParameterName = "TimeSeriesDataStore";
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static String dbuserParameterName = "user";
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static String dbpasswordParameterName = "password";
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static String dburlParameterName = "FishBase";
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static String dburlParameterName = "STOREURL";
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static String inputTableParameter = "InputTable";
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static String outputTableParameter = "OutputTable";
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@ -51,42 +30,53 @@ public class MapsCreator extends StandardLocalExternalAlgorithm {
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static String csquareParameter = "csquaresDimension";
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static String probabilityParameter = "Probability";
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static String infoParameter = "Info";
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static String resolutionParameter = "Resolution";
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static String layerNameParameter = "MapName";
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static int maxNPoints = 19000;
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static int maxNPoints = 259000;
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SessionFactory gisdbconnection = null;
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SessionFactory smdbconnection = null;
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private static String createTable = "create table %1$s (geomid serial, x real, y real, probability real);";
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private static String columnsNames = " geomid, x , y, probability";
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private static String createProbTable = "create table %1$s (geomid serial, x real, y real, probability real);";
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private static String columnsProbNames = " geomid, x , y, probability, the_geom";
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private static String createInfoTable = "create table %1$s (geomid serial, x real, y real, info character varying);";
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private static String columnsInfoNames = " geomid, x , y, info, the_geom";
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private static String addGeometryColumn = "Select AddGeometryColumn('%1$s','the_geom',4326,'POLYGON',2);";
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static String makeSquare = "ST_SetSRID(ST_MakePolygon(ST_GeomFromText('LINESTRING(%1$s ,%2$s, %3$s, %4$s, %1$s)')),4326)";
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@Override
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static String makeSquare = "ST_GeomFromText('POLYGON((%1$s ,%2$s, %3$s, %4$s, %1$s))',4326)";
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//changeable parameters for application purposes
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String datastore = "";
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String defaultStyle = "";
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String workspace = "";
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String username = "";
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String purpose = "";
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String credits = "";
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String keyword = "";
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@Override
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public String getDescription() {
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return "A transducer algorithm to produce a GIS map either from a probability distribution or from a set of points. A maximum of " + maxNPoints + " is allowed";
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}
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@Override
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public void init() throws Exception {
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log("MAPS_CREATOR");
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}
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public abstract void init() throws Exception;
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@Override
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protected void process() throws Exception {
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try {
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log("Beginning process");
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log("Using scope:"+config.getGcubeScope());
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//initialize Gis DB parameters
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String databaseJdbc = getInputParameter(dburlParameterName);
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String databaseUser = getInputParameter(dbuserParameterName);
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String databasePwd = getInputParameter(dbpasswordParameterName);
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log("GIS Database Parameters to use: " + databaseJdbc + " , " + databaseUser);
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double resolution = Double.parseDouble(config.getParam(resolutionParameter));
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log("Resolution:" + resolution);
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//getting resolution
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String res$ = config.getParam(resolutionParameter);
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double resolution = res$!=null?Double.parseDouble(res$):0;
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//connection to the GIS DB
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log("Connecting to gisDB...");
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AlgorithmConfiguration gisconfig = new AlgorithmConfiguration();
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gisconfig.setParam("DatabaseDriver", "org.postgresql.Driver");
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@ -94,87 +84,98 @@ public class MapsCreator extends StandardLocalExternalAlgorithm {
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gisconfig.setParam("DatabaseUserName", databaseUser);
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gisconfig.setParam("DatabasePassword", databasePwd);
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gisconfig.setConfigPath(config.getConfigPath());
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gisdbconnection = DatabaseUtils.initDBSession(gisconfig);
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// connect to the GIS DB
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log("Initialized gisDBConnection!");
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// connect to the SM DB
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smdbconnection = DatabaseUtils.initDBSession(config);
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log("Initialized SMDBConnection!");
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//select info to attach
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String infoPar = config.getParam(probabilityParameter);
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if (infoPar == null)
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infoPar = config.getParam(infoParameter);
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// points retrieval
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List<Object> points = null;
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log("Retrieving points..");
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if (config.getParam(xParameter) != null && config.getParam(yParameter) != null) {
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log("..from coordinates");
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// select the points from the SM DB up to a maximum of 190000 points
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points = DatabaseFactory.executeSQLQuery("select " + config.getParam(xParameter) + "," + config.getParam(yParameter) + "," + config.getParam(probabilityParameter) + " from " + config.getParam(inputTableParameter) + " limit " + maxNPoints, smdbconnection);
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points = DatabaseFactory.executeSQLQuery("select " + config.getParam(xParameter) + "," + config.getParam(yParameter) + "," +infoPar + " from " + config.getParam(inputTableParameter) + " limit " + maxNPoints, smdbconnection);
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}
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//points from csquares
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else if (config.getParam(csquareParameter)!=null){
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log("..from csquares");
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List<Object> csquares= DatabaseFactory.executeSQLQuery("select " + config.getParam(csquareParameter) +" from " + config.getParam(inputTableParameter) + " limit " + maxNPoints, smdbconnection);
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String queryCsquare = "select " + config.getParam(csquareParameter) + "," + infoPar +" from " + config.getParam(inputTableParameter) + " limit " + maxNPoints;
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List<Object> csquares= DatabaseFactory.executeSQLQuery(queryCsquare, smdbconnection);
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points = new ArrayList<Object>();
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//build points from csquares
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for (Object csquare:csquares){
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CSquare c = it.cnr.aquamaps.CSquare.apply(""+csquare);
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Object[] csquareandprob = (Object[]) csquare;
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CSquare c = it.cnr.aquamaps.CSquare.apply(""+csquareandprob[0]);
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if (resolution==0)
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resolution=c.size();
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// x,y
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Iterator<Object> iterator = c.center().valuesIterator();
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double x = Double.parseDouble(""+iterator.next());
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double y = Double.parseDouble(""+iterator.next());
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Object[] pair = {x,y};
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String x = ""+iterator.next();
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String y = ""+iterator.next();
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String prob = ""+csquareandprob[1];
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Object[] pair = {x,y,prob};
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points.add(pair);
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}
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log("Points built from csquares!");
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}
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//GIS Table creation
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log("Creating GIS table");
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String gisTableName = "stat" + UUID.randomUUID().toString().replace("-", "");
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// create a table on the gis db
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String createTable$ = String.format(createTable, gisTableName);
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String createTable$ = String.format(createProbTable, gisTableName);
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String columnNames$ = columnsProbNames;
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if (config.getParam(probabilityParameter)==null){
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createTable$ = String.format(createInfoTable, gisTableName);
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columnNames$=columnsInfoNames;
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}
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log(createTable$);
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//drop previous table
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try {
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(gisTableName), gisdbconnection);
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} catch (Exception e) {
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log("Impossible to drop table:" + e.getLocalizedMessage());
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}
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DatabaseFactory.executeSQLUpdate(String.format(createTable, gisTableName), gisdbconnection);
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//table creation
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DatabaseFactory.executeSQLUpdate(createTable$, gisdbconnection);
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DatabaseFactory.executeSQLQuery(String.format(addGeometryColumn, gisTableName), gisdbconnection);
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log("Fulfilling elements");
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log("Resolution:" + resolution);
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//points fulfilling
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List<String[]> values = new ArrayList<String[]>();
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int i = 0;
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List<Object> squares = new ArrayList<Object>();
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for (Object point : points) {
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Object[] elements = (Object[]) point;
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double x = Double.parseDouble("" + elements[0]);
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double y = Double.parseDouble("" + elements[1]);
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String probS = "" + elements[2];
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double x1 = Math.max(-180, x - resolution);
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double x2 = Math.min(180, x + resolution);
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double y1 = Math.max(-90, y - resolution);
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double y2 = Math.max(180, y + resolution);
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double x1 = x - resolution;
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double x2 = x + resolution;
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double y1 = y - resolution;
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double y2 = y + resolution;
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String square = String.format(makeSquare, "" + x1 + " " + y1, x1 + " " + y2, x2 + " " + y2, x2 + " " + y1);
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Object[] pair = new Object[2];
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pair[0] = "" + i;
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pair[1] = square;
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squares.add(pair);
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// insert into stat34cbc4ce921a410fbf4bac0d9c21fcf5 ( x , y, probability, the_geom) values ('0.25','0.25','34.0', ST_SetSRID(ST_MakePolygon(ST_GeomFromText('LINESTRING(-0.25 -0.25 ,-0.25 180.0, 0.75 180.0, 0.75 -0.25, -0.25 -0.25)')),4326))
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String[] selements = { "" + i, "" + x, "" + y, probS };
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// System.out.println(square);
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String[] selements = { "" + i, "" + x, "" + y, probS,square };
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values.add(selements);
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i++;
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}
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log("Writing chunks");
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// write chunks into the DB
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DatabaseUtils.insertChunksIntoTable(gisTableName, columnsNames, values, 5000, gisdbconnection);
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log("Writing Geometries");
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.insertIntoColumn(gisTableName, "geomid", "the_geom", squares), gisdbconnection);
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insertGeoChunksIntoTable(gisTableName, columnNames$, values, 5000, gisdbconnection);
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log("Publishing Table");
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String username = config.getParam("ServiceUserName");
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if (username == null)
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username = "statistical.manager";
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String usernameP = config.getParam("ServiceUserName");
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if (usernameP != null)
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username = usernameP;
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String layerName = config.getParam(layerNameParameter);
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PublishResponse response = publishTable(config.getGcubeScope(), gisTableName, resolution, username, layerName);
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PublishResponse response = PolyMapMetadata.publishTable(config.getGcubeScope(), gisTableName, resolution, username, layerName, defaultStyle, workspace, datastore, purpose, credits, keyword);
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//analyzing response
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if (response == null) {
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log("Error in generating map - dropping gis table");
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try {
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@ -185,13 +186,18 @@ public class MapsCreator extends StandardLocalExternalAlgorithm {
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}
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throw new Exception("Impossible to publish on GeoNetwork or GeoServer: " + gisTableName);
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} else {
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//writing output
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addOutputString("GIS map title", layerName);
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addOutputString("GIS map UUID", "" + response.getPublishedMetadata().getFileIdentifier());
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addOutputString("Associated Geospatial Table", gisTableName);
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addOutputString("Generated by ", username);
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addOutputString("Resolution", "" + resolution);
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addOutputString("Style", "" + defaultStyle);
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addOutputString("Keyword", "" + keyword);
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}
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log("Output:"+outputParameters);
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log("All Done!");
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} catch (Exception e) {
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e.printStackTrace();
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throw e;
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@ -204,132 +210,53 @@ public class MapsCreator extends StandardLocalExternalAlgorithm {
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}
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public PublishResponse publishTable(String scope, String tableName, double resolution, String username, String layerName) throws Exception {
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String datastore = "timeseriesws";
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String defaultStyle = "Species_prob";
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String workspace = "aquamaps";
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GSFeatureTypeEncoder fte = new GSFeatureTypeEncoder();
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fte.setEnabled(true);
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fte.setLatLonBoundingBox(-180.0, -90.0, 180.0, 90.0, crs);
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fte.setName(tableName);
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fte.setNativeCRS(crs);
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GSLayerEncoder le = new GSLayerEncoder();
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le.setDefaultStyle(defaultStyle);
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le.setEnabled(true);
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GcubeISOMetadata meta = fillMeta(resolution, username, layerName, scope);
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GISInterface gis = GISInterface.get();
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Configuration gnConfig = gis.getGeoNetworkReader().getConfiguration();
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log("Using the following GNetwork:" + gnConfig.getGeoNetworkEndpoint());
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PublishResponse resp = gis.publishDBTable(workspace, datastore, fte, le, meta.getMetadata(), new GNInsertConfiguration(gnConfig.getScopeGroup() + "", "datasets", "_none_", true), LoginLevel.DEFAULT);
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log(resp);
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log("ID:" + resp.getReturnedMetaId());
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log("Result:" + resp.getMetaOperationResult());
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if (resp.getReturnedMetaId()==0)
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return null;
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else
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return resp;
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public static void insertGeoChunksIntoTable(String table, String columnsNames, List<String[]> values, int chunkSize,SessionFactory dbconnection) throws Exception{
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int valuesize = values.size();
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StringBuffer sb = new StringBuffer();
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int stopIndex =0;
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for (int i=0;i<valuesize;i++){
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String[] row = values.get(i);
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sb.append("(");
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for (int j=0;j<row.length-1;j++){
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String preprow = row[j].replaceAll("^'", "").replaceAll("'$", "");
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preprow=preprow.replace("'", ""+(char)96);
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sb.append("'"+preprow+"'");
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sb.append(",");
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}
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//append geometry
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sb.append(row[row.length-1]);
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sb.append(")");
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if (stopIndex>0 && stopIndex%chunkSize==0){
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.insertFromBuffer(table, columnsNames, sb), dbconnection);
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stopIndex=chunkSize;
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sb = new StringBuffer();
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}
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else if (i<valuesize-1)
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sb.append(",");
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}
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if (stopIndex<valuesize-1){
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if (sb.length()>0){
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try{
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.insertFromBuffer(table, columnsNames, sb), dbconnection);
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}catch(Exception e){
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System.out.println("Query:"+sb);
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throw e;
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}
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}
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}
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}
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private GcubeISOMetadata fillMeta(double resolution, String username, String title, String scope) throws Exception {
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if (scope == null)
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scope = ScopeProvider.instance.get();
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ScopeProvider.instance.set(scope);
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GcubeISOMetadata meta = new GcubeISOMetadata();
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meta.setAbstractField("This metadata is just a test");
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meta.setCreationDate(new Date(System.currentTimeMillis()));
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meta.setExtent((DefaultExtent) DefaultExtent.WORLD);
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meta.setGeometricObjectType(GeometricObjectType.SURFACE);
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meta.setPresentationForm(PresentationForm.MAP_DIGITAL);
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meta.setPurpose("Publish Geometric Layer");
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meta.setResolution(resolution);
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if (title == null || title.length() == 0)
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meta.setTitle("Probability Distribution");
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else
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meta.setTitle(title);
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meta.setTopologyLevel(TopologyLevel.GEOMETRY_ONLY);
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meta.setUser(username);
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meta.addCredits("Generated via the Statistical Manager Service");
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meta.addGraphicOverview("http://www.d4science.org/D4ScienceOrg-Social-theme/images/custom/D4ScienceInfrastructure.png");
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Thesaurus generalThesaurus = meta.getConfig().getThesauri().get("General");
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meta.addKeyword(title, generalThesaurus);
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meta.addKeyword(username, generalThesaurus);
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meta.addKeyword("StatisticalManager", generalThesaurus);
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meta.addKeyword("Probability Distribution", generalThesaurus);
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meta.addTopicCategory(TopicCategory.BIOTA);
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return meta;
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}
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public static void main(String[] args) throws Exception {
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath("./cfg/");
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config.setPersistencePath("./cfg/");
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config.setGcubeScope("/gcube");
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config.setParam("DatabaseUserName", "utente");
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config.setParam("DatabasePassword", "d4science");
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config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
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config.setParam(dburlParameterName, "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb");
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||||
// jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb, DatabasePassword=d4science, DatabaseUserName=utente, password=d4science2
|
||||
// config.setParam(dburlParameterName,"jdbc:postgresql://146.48.122.125/timeseriesgisdb");
|
||||
config.setParam(dbuserParameterName, "postgres");
|
||||
config.setParam(dbpasswordParameterName, "d4science2");
|
||||
|
||||
config.setParam(inputTableParameter, "occcluster_id_59005678_4863_49ba_9c66_ebac80829da3");
|
||||
config.setParam(xParameter, "centerlong");
|
||||
config.setParam(yParameter, "centerlat");
|
||||
config.setParam(probabilityParameter, "faoaream");
|
||||
config.setParam(resolutionParameter, "0.5");
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
config.setParam(layerNameParameter, "Generic Species");
|
||||
|
||||
MapsCreator maps = new MapsCreator();
|
||||
maps.setConfiguration(config);
|
||||
maps.compute();
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void shutdown() {
|
||||
|
||||
log("shutdown invoked!");
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try {
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
addStringInput(layerNameParameter, "The name of the layer to produce", "Statistical Prob. Distribution");
|
||||
InputTable tinput = new InputTable(templates, inputTableParameter, "The table information to geo-spatialize");
|
||||
ColumnType xColumn = new ColumnType(inputTableParameter, xParameter, "The column containing longitude information", "", false);
|
||||
ColumnType yColumn = new ColumnType(inputTableParameter, yParameter, "The column containing latitude information", "", false);
|
||||
ColumnType probabilityDimension = new ColumnType(inputTableParameter, probabilityParameter, "The column containing probability information", "", false);
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(xColumn);
|
||||
inputs.add(yColumn);
|
||||
inputs.add(probabilityDimension);
|
||||
addDoubleInput(resolutionParameter, "The map resolution in degrees", "0.5");
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public StatisticalType getOutput() {
|
||||
|
||||
return null;
|
||||
}
|
||||
protected abstract void setInputParameters();
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,76 @@
|
|||
package org.gcube.dataanalysis.geo.algorithms;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
|
||||
|
||||
public class PointsMapsCreator extends MapsCreator {
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
log("MAPS_CREATOR");
|
||||
datastore = "timeseriesws";
|
||||
defaultStyle = "point";
|
||||
workspace = "aquamaps";
|
||||
username = "statistical.manager";
|
||||
purpose = "To Publish Geometric Layers for Points Maps";
|
||||
credits = "Generated via the Statistical Manager Service";
|
||||
keyword = "Points Map";
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try {
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
addStringInput(layerNameParameter, "The name of the layer to produce", "Statistical Prob. Distribution");
|
||||
InputTable tinput = new InputTable(templates, inputTableParameter, "The table information to geo-spatialize");
|
||||
ColumnType xColumn = new ColumnType(inputTableParameter, xParameter, "The column containing longitude information", "", false);
|
||||
ColumnType yColumn = new ColumnType(inputTableParameter, yParameter, "The column containing latitude information", "", false);
|
||||
ColumnType customDimension = new ColumnType(inputTableParameter, infoParameter, "The column containing information you want to attach to each point", "", false);
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(xColumn);
|
||||
inputs.add(yColumn);
|
||||
inputs.add(customDimension);
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./cfg/");
|
||||
config.setGcubeScope("/gcube");
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
||||
config.setParam(dburlParameterName, "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb");
|
||||
config.setParam(dbuserParameterName, "postgres");
|
||||
config.setParam(dbpasswordParameterName, "d4science2");
|
||||
|
||||
config.setParam(inputTableParameter, "occurrence_species_id_fb60ce42_1704_43f9_91a3_2df7d82b1b96");
|
||||
config.setParam(xParameter, "decimallongitude");
|
||||
config.setParam(yParameter, "decimallatitude");
|
||||
config.setParam(infoParameter, "scientificname");
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
config.setParam(layerNameParameter, "Generic Species");
|
||||
|
||||
MapsCreator maps = new PointsMapsCreator();
|
||||
maps.setConfiguration(config);
|
||||
maps.init();
|
||||
maps.compute();
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
package org.gcube.dataanalysis.geo.algorithms;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
|
||||
|
||||
public class PolygonMapsCreator extends MapsCreator {
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
log("MAPS_CREATOR");
|
||||
datastore = "timeseriesws";
|
||||
defaultStyle = "polygon";
|
||||
workspace = "aquamaps";
|
||||
username = "statistical.manager";
|
||||
purpose = "To Publish Geometric Layers for Polygonal Maps";
|
||||
credits = "Generated via the Statistical Manager Service";
|
||||
keyword = "Polygonal Map";
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try {
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
addStringInput(layerNameParameter, "The name of the layer to produce", "Statistical Prob. Distribution");
|
||||
InputTable tinput = new InputTable(templates, inputTableParameter, "The table information to geo-spatialize");
|
||||
ColumnType xColumn = new ColumnType(inputTableParameter, xParameter, "The column containing longitude information", "", false);
|
||||
ColumnType yColumn = new ColumnType(inputTableParameter, yParameter, "The column containing latitude information", "", false);
|
||||
ColumnType customDimension = new ColumnType(inputTableParameter, infoParameter, "The column containing information you want to attach to each polygon", "", false);
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(xColumn);
|
||||
inputs.add(yColumn);
|
||||
inputs.add(customDimension);
|
||||
addDoubleInput(resolutionParameter, "The map resolution in degrees", "0.5");
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./cfg/");
|
||||
config.setGcubeScope("/gcube");
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
||||
config.setParam(dburlParameterName, "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb");
|
||||
config.setParam(dbuserParameterName, "postgres");
|
||||
config.setParam(dbpasswordParameterName, "d4science2");
|
||||
|
||||
config.setParam(inputTableParameter, "occcluster_id_59005678_4863_49ba_9c66_ebac80829da3");
|
||||
config.setParam(xParameter, "centerlong");
|
||||
config.setParam(yParameter, "centerlat");
|
||||
config.setParam(infoParameter, "faoaream");
|
||||
config.setParam(resolutionParameter, "0.5");
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
config.setParam(layerNameParameter, "Generic Species");
|
||||
|
||||
MapsCreator maps = new PolygonMapsCreator();
|
||||
maps.setConfiguration(config);
|
||||
maps.init();
|
||||
maps.compute();
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,74 @@
|
|||
package org.gcube.dataanalysis.geo.algorithms;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
|
||||
|
||||
public class SpeciesDistributionsMapsCreatorFromCsquares extends MapsCreator {
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
log("MAPS_CREATOR");
|
||||
datastore = "timeseriesws";
|
||||
defaultStyle = "Species_prob";
|
||||
workspace = "aquamaps";
|
||||
username = "statistical.manager";
|
||||
purpose = "To Publish Geometric Layers for Species Distribution Maps";
|
||||
credits = "Generated via the Statistical Manager Service";
|
||||
keyword = "Species Probability Distribution";
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try {
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
addStringInput(layerNameParameter, "The name of the layer to produce", "Statistical Prob. Distribution");
|
||||
InputTable tinput = new InputTable(templates, inputTableParameter, "The table information to geo-spatialize");
|
||||
ColumnType xColumn = new ColumnType(inputTableParameter, csquareParameter, "The column containing csquare codes", "", false);
|
||||
ColumnType probabilityDimension = new ColumnType(inputTableParameter, probabilityParameter, "The column containing probability information", "", false);
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(xColumn);
|
||||
inputs.add(probabilityDimension);
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./cfg/");
|
||||
config.setGcubeScope("/gcube");
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
||||
config.setParam(dburlParameterName, "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb");
|
||||
config.setParam(dbuserParameterName, "postgres");
|
||||
config.setParam(dbpasswordParameterName, "d4science2");
|
||||
|
||||
config.setParam(inputTableParameter, "hspec_id_4cd0644e_46c5_4b33_b8fa_85b0c6b01982");
|
||||
config.setParam(csquareParameter, "csquarecode");
|
||||
config.setParam(probabilityParameter, "probability");
|
||||
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
config.setParam(layerNameParameter, "Generic Species");
|
||||
|
||||
MapsCreator maps = new SpeciesDistributionsMapsCreatorFromCsquares();
|
||||
maps.setConfiguration(config);
|
||||
maps.init();
|
||||
maps.compute();
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
package org.gcube.dataanalysis.geo.algorithms;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
|
||||
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
|
||||
|
||||
public class SpeciesDistributionsMapsCreatorFromPoints extends MapsCreator {
|
||||
|
||||
@Override
|
||||
public void init() throws Exception {
|
||||
log("MAPS_CREATOR");
|
||||
datastore = "timeseriesws";
|
||||
defaultStyle = "Species_prob";
|
||||
workspace = "aquamaps";
|
||||
username = "statistical.manager";
|
||||
purpose = "To Publish Geometric Layers for Species Distribution Maps";
|
||||
credits = "Generated via the Statistical Manager Service";
|
||||
keyword = "Species Probability Distribution";
|
||||
}
|
||||
|
||||
@Override
|
||||
protected void setInputParameters() {
|
||||
try {
|
||||
List<TableTemplates> templates = new ArrayList<TableTemplates>();
|
||||
addRemoteDatabaseInput(databaseParameterName, dburlParameterName, dbuserParameterName, dbpasswordParameterName, "driver", "dialect");
|
||||
templates.add(TableTemplates.GENERIC);
|
||||
addStringInput(layerNameParameter, "The name of the layer to produce", "Statistical Prob. Distribution");
|
||||
InputTable tinput = new InputTable(templates, inputTableParameter, "The table information to geo-spatialize");
|
||||
ColumnType xColumn = new ColumnType(inputTableParameter, xParameter, "The column containing longitude information", "", false);
|
||||
ColumnType yColumn = new ColumnType(inputTableParameter, yParameter, "The column containing latitude information", "", false);
|
||||
ColumnType probabilityDimension = new ColumnType(inputTableParameter, probabilityParameter, "The column containing probability information", "", false);
|
||||
|
||||
inputs.add(tinput);
|
||||
inputs.add(xColumn);
|
||||
inputs.add(yColumn);
|
||||
inputs.add(probabilityDimension);
|
||||
addDoubleInput(resolutionParameter, "The map resolution in degrees", "0.5");
|
||||
DatabaseType.addDefaultDBPars(inputs);
|
||||
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
config.setConfigPath("./cfg/");
|
||||
config.setPersistencePath("./cfg/");
|
||||
config.setGcubeScope("/gcube");
|
||||
config.setParam("DatabaseUserName", "utente");
|
||||
config.setParam("DatabasePassword", "d4science");
|
||||
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
||||
|
||||
config.setParam(dburlParameterName, "jdbc:postgresql://geoserver-test.d4science-ii.research-infrastructures.eu/timeseriesgisdb");
|
||||
config.setParam(dbuserParameterName, "postgres");
|
||||
config.setParam(dbpasswordParameterName, "d4science2");
|
||||
|
||||
config.setParam(inputTableParameter, "occcluster_id_59005678_4863_49ba_9c66_ebac80829da3");
|
||||
config.setParam(xParameter, "centerlong");
|
||||
config.setParam(yParameter, "centerlat");
|
||||
config.setParam(probabilityParameter, "faoaream");
|
||||
config.setParam(resolutionParameter, "0.5");
|
||||
config.setParam("ServiceUserName", "gianpaolo.coro");
|
||||
config.setParam(layerNameParameter, "Generic Species");
|
||||
|
||||
MapsCreator maps = new SpeciesDistributionsMapsCreatorFromPoints();
|
||||
maps.setConfiguration(config);
|
||||
maps.init();
|
||||
maps.compute();
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
package org.gcube.dataanalysis.geo.meta;
|
||||
|
||||
import it.geosolutions.geonetwork.util.GNInsertConfiguration;
|
||||
import it.geosolutions.geoserver.rest.encoder.GSLayerEncoder;
|
||||
import it.geosolutions.geoserver.rest.encoder.feature.GSFeatureTypeEncoder;
|
||||
|
||||
import java.util.Date;
|
||||
|
||||
import org.gcube.common.scope.api.ScopeProvider;
|
||||
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
||||
import org.gcube.spatial.data.geonetwork.LoginLevel;
|
||||
import org.gcube.spatial.data.geonetwork.configuration.Configuration;
|
||||
import org.gcube.spatial.data.geonetwork.iso.GcubeISOMetadata;
|
||||
import org.gcube.spatial.data.geonetwork.iso.Thesaurus;
|
||||
import org.gcube.spatial.data.gis.GISInterface;
|
||||
import org.gcube.spatial.data.gis.model.report.PublishResponse;
|
||||
import org.geotoolkit.metadata.iso.extent.DefaultExtent;
|
||||
import org.opengis.metadata.citation.PresentationForm;
|
||||
import org.opengis.metadata.identification.TopicCategory;
|
||||
import org.opengis.metadata.spatial.GeometricObjectType;
|
||||
import org.opengis.metadata.spatial.TopologyLevel;
|
||||
|
||||
public class PolyMapMetadata {
|
||||
|
||||
private static final String crs = "GEOGCS[\"WGS 84\", DATUM[\"World Geodetic System 1984\", SPHEROID[\"WGS 84\", 6378137.0, 298.257223563, AUTHORITY[\"EPSG\",\"7030\"]]," + "AUTHORITY[\"EPSG\",\"6326\"]], PRIMEM[\"Greenwich\", 0.0, AUTHORITY[\"EPSG\",\"8901\"]], UNIT[\"degree\", 0.017453292519943295]," + "AXIS[\"Geodetic longitude\", EAST], AXIS[\"Geodetic latitude\", NORTH], AUTHORITY[\"EPSG\",\"4326\"]]";
|
||||
|
||||
public static PublishResponse publishTable(String scope, String tableName, double resolution, String username, String layerName, String defaultStyle, String workspace, String datastore, String purpose, String credits, String keyword) throws Exception {
|
||||
|
||||
GSFeatureTypeEncoder fte = new GSFeatureTypeEncoder();
|
||||
fte.setEnabled(true);
|
||||
fte.setLatLonBoundingBox(-180.0, -90.0, 180.0, 90.0, crs);
|
||||
fte.setName(tableName);
|
||||
fte.setNativeCRS(crs);
|
||||
GSLayerEncoder le = new GSLayerEncoder();
|
||||
le.setDefaultStyle(defaultStyle);
|
||||
le.setEnabled(true);
|
||||
GcubeISOMetadata meta = fillMeta(resolution, username, layerName, scope, tableName,purpose, credits, keyword);
|
||||
GISInterface gis = GISInterface.get();
|
||||
Configuration gnConfig = gis.getGeoNetworkReader().getConfiguration();
|
||||
AnalysisLogger.getLogger().debug("Using the following GNetwork:" + gnConfig.getGeoNetworkEndpoint());
|
||||
PublishResponse resp = gis.publishDBTable(workspace, datastore, fte, le, meta.getMetadata(), new GNInsertConfiguration(gnConfig.getScopeGroup() + "", "datasets", "_none_", true), LoginLevel.DEFAULT);
|
||||
AnalysisLogger.getLogger().debug(resp);
|
||||
AnalysisLogger.getLogger().debug("ID:" + resp.getReturnedMetaId());
|
||||
AnalysisLogger.getLogger().debug("Result:" + resp.getMetaOperationResult());
|
||||
if (resp.getReturnedMetaId()==0)
|
||||
return null;
|
||||
else
|
||||
return resp;
|
||||
}
|
||||
|
||||
|
||||
private static GcubeISOMetadata fillMeta(double resolution, String username, String title, String scope, String tableName ,String purpose, String credits, String keyword) throws Exception {
|
||||
|
||||
if (scope == null)
|
||||
scope = ScopeProvider.instance.get();
|
||||
|
||||
ScopeProvider.instance.set(scope);
|
||||
|
||||
GcubeISOMetadata meta = new GcubeISOMetadata();
|
||||
meta.setAbstractField("This metadata has been automatically generated from the Statistical Manager on the basis of a distribution of points and according the resolution of "+resolution+" degrees.");
|
||||
meta.setCreationDate(new Date(System.currentTimeMillis()));
|
||||
meta.setExtent((DefaultExtent) DefaultExtent.WORLD);
|
||||
meta.setGeometricObjectType(GeometricObjectType.SURFACE);
|
||||
meta.setPresentationForm(PresentationForm.MAP_DIGITAL);
|
||||
meta.setPurpose(purpose);
|
||||
meta.setResolution(resolution);
|
||||
if (title == null || title.length() == 0)
|
||||
meta.setTitle("Distribution");
|
||||
else
|
||||
meta.setTitle(title);
|
||||
|
||||
meta.setTopologyLevel(TopologyLevel.GEOMETRY_ONLY);
|
||||
meta.setUser(username);
|
||||
|
||||
|
||||
meta.addGraphicOverview("http://www.d4science.org/D4ScienceOrg-Social-theme/images/custom/D4ScienceInfrastructure.png");
|
||||
meta.addCredits(credits);
|
||||
Thesaurus generalThesaurus = meta.getConfig().getThesauri().get("General");
|
||||
meta.addKeyword(title, generalThesaurus);
|
||||
meta.addKeyword(username, generalThesaurus);
|
||||
meta.addKeyword("StatisticalManager", generalThesaurus);
|
||||
meta.addKeyword(keyword, generalThesaurus);
|
||||
meta.addKeyword(tableName,generalThesaurus);
|
||||
meta.addTopicCategory(TopicCategory.BIOTA);
|
||||
return meta;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue